Plant Circular RNA Database

Detail information of AT5G12230_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT5G12230_circ_g.9
					
						ID in PlantcircBase
						ath_circ_037771
					
						Alias
						At_ciR1505, Ath_circ_FC3252, Ath_circ_FC3253, Ath_circ_FC3254
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 3954375-3955343  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT5G12230						
					
						Parent gene annotation
						
							Mediator of RNA polymerase II transcription subunit 19a
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G12230_circ_g.1 AT5G12230_circ_g.2 AT5G12230_circ_g.3 AT5G12230_circ_g.4 AT5G12230_circ_g.5 AT5G12230_circ_g.6 AT5G12230_circ_g.7 AT5G12230_circ_g.8 AT5G12230_circ_g.10 						
					
						Support reads
						8/3/5
					
						Tissues
						leaf/inflorescences, whole_plant/seedlings
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						AT5G12230.1:3

General Information
CircRNA Name	AT5G12230_circ_g.9
ID in PlantcircBase	ath_circ_037771
Alias	At_ciR1505, Ath_circ_FC3252, Ath_circ_FC3253, Ath_circ_FC3254
Organism	Arabidpsis thaliana
Position	chr5: 3954375-3955343 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT5G12230
Parent gene annotation	Mediator of RNA polymerase II transcription subunit 19a
Parent gene strand	-
Alternative splicing	AT5G12230_circ_g.1 AT5G12230_circ_g.2 AT5G12230_circ_g.3 AT5G12230_circ_g.4 AT5G12230_circ_g.5 AT5G12230_circ_g.6 AT5G12230_circ_g.7 AT5G12230_circ_g.8 AT5G12230_circ_g.10
Support reads	8/3/5
Tissues	leaf/inflorescences, whole_plant/seedlings
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	AT5G12230.1:3

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							CGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATT
TCTTTTGCATGATCACTGGCTCACTGCATATATATCcttatcatgatgtttcttagaatgatca
cccgaatcatggtggccatttttgtccttctttctgtctcggtccttgtctttatctttatctt
tgcttcta

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 613
Transcript exons: 3954375-3954611,3954846-3955135,3955258-3955343
CTTATCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTG
TCTCGGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTAT
GCTCTCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGA
CTCACTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCTGGGGGTAATTCAACAGGA
GTCATATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATATCAAAAGGCTGGATGCGAATAT
TAGTCTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCT
GATCTCTGTGTCCCCAACCACATTATGAAGATAATGGGAATCTGATAAAGAAACAGGAAGAGAT
TTCTTGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGAGATATAAGATCCGCAGCACCGC
ACAACTCTCTTGGACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAAT
TTCTTTTGCATGATCACTGGCTCACTGCATATATATC
						
					

						Genomic sequence
						
							CTTATCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTG
TCTCGGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTAT
GCTCTCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGA
CTCACTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCCTGAAAGAAGAATAGTACC
AAGGTCAATCATCTCCATAGGACACCCAGATGTAATTCACATTACTAGGGAAAGATTCTCAATT
AACCAAAGAACTTGATGTTACAGGAAATAGGACATTCATTACTGAGCCAGTTTTTAAGTTCAAT
GTAATGGCAAATACTGTTACTCTTATGAAAAGAAGGACATTTAAAACTCAAAACACCAAGAGAG
AGTGAGAAAGATCAGATTCTTACTGGGGGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAG
ACTCCTGAAGCTCATCTATATCAAAAGGCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATAT
GCTCTCAATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACA
TTATGAAGATAATGGGAATCTGATAAAGAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGT
GTTGCACTAGTTTGAATTGAGATATAAGATCCGCAGCACCGCACAACTCTCTTGGACCTGCACT
TGAAACAAACAACACATTGACCTCAAGGTGAGCCAAAGGGGAAAACAAAGGACAACGAGCTACA
AAAAAAATAACTTCACGAACTGAAGAAGCTCCAAATTCGAAACCAATGTACCTCCAAATTTTAA
ACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGC
ATATATATC
						
					

			
		

Sequences
Splice junction sequence	CGAAACCAATGTACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATT TCTTTTGCATGATCACTGGCTCACTGCATATATATCcttatcatgatgtttcttagaatgatca cccgaatcatggtggccatttttgtccttctttctgtctcggtccttgtctttatctttatctt tgcttcta
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 613 Transcript exons: 3954375-3954611,3954846-3955135,3955258-3955343 CTTATCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTG TCTCGGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTAT GCTCTCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGA CTCACTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCTGGGGGTAATTCAACAGGA GTCATATCATTTAGTTGGAAAGACTCCTGAAGCTCATCTATATCAAAAGGCTGGATGCGAATAT TAGTCTCCCGGCTCTGTGATATGCTCTCAATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCT GATCTCTGTGTCCCCAACCACATTATGAAGATAATGGGAATCTGATAAAGAAACAGGAAGAGAT TTCTTGCAAAAGAATTCATGGTGTTGCACTAGTTTGAATTGAGATATAAGATCCGCAGCACCGC ACAACTCTCTTGGACCTCCAAATTTTAAACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAAT TTCTTTTGCATGATCACTGGCTCACTGCATATATATC
Genomic sequence	CTTATCATGATGTTTCTTAGAATGATCACCCGAATCATGGTGGCCATTTTTGTCCTTCTTTCTG TCTCGGTCCTTGTCTTTATCTTTATCTTTGCTTCTATCTTTATGTTTGTGCTTGTGCTTCTTAT GCTCTCTATCTTTGTCTTTATCCCTGTCCTTGTGTTTCTTATGTTTCCTGTCCCTATCTTTCGA CTCACTTTTTGACTTAGACGGAATTGTAGGAGCTCCCTTCTCTGCCTGAAAGAAGAATAGTACC AAGGTCAATCATCTCCATAGGACACCCAGATGTAATTCACATTACTAGGGAAAGATTCTCAATT AACCAAAGAACTTGATGTTACAGGAAATAGGACATTCATTACTGAGCCAGTTTTTAAGTTCAAT GTAATGGCAAATACTGTTACTCTTATGAAAAGAAGGACATTTAAAACTCAAAACACCAAGAGAG AGTGAGAAAGATCAGATTCTTACTGGGGGTAATTCAACAGGAGTCATATCATTTAGTTGGAAAG ACTCCTGAAGCTCATCTATATCAAAAGGCTGGATGCGAATATTAGTCTCCCGGCTCTGTGATAT GCTCTCAATAAGCTGATCTAATTGCATTCCTTCTCCTTTTCTGATCTCTGTGTCCCCAACCACA TTATGAAGATAATGGGAATCTGATAAAGAAACAGGAAGAGATTTCTTGCAAAAGAATTCATGGT GTTGCACTAGTTTGAATTGAGATATAAGATCCGCAGCACCGCACAACTCTCTTGGACCTGCACT TGAAACAAACAACACATTGACCTCAAGGTGAGCCAAAGGGGAAAACAAAGGACAACGAGCTACA AAAAAAATAACTTCACGAACTGAAGAAGCTCCAAATTCGAAACCAATGTACCTCCAAATTTTAA ACGTTCAGGCTCCATCTTCTCTATCGCACTCTGAATTTCTTTTGCATGATCACTGGCTCACTGC ATATATATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.526648422

Conservation Information
Conserved circRNAs	NA
PMCS	0.526648422

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to heat stress

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to heat stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT5G12230_circ_g.9

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